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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 10:27, 17 September 2013


Full id: C86_colon_carcinoid_small_neuroectodermal_giant_large_neuroepithelioma



Phase1 CAGE Peaks

Hg19::chr10:2328652..2328660,+p@chr10:2328652..2328660
+
Hg19::chr10:7144649..7144656,-p@chr10:7144649..7144656
-
Hg19::chr10:72303802..72303817,+p@chr10:72303802..72303817
+
Hg19::chr11:90181710..90181723,+p@chr11:90181710..90181723
+
Hg19::chr12:27932408..27932428,+p17@KLHDC5
Hg19::chr12:65277536..65277559,+p1@FLJ41278
Hg19::chr12:65277574..65277589,+p2@FLJ41278
Hg19::chr12:65447288..65447294,+p@chr12:65447288..65447294
+
Hg19::chr12:65466870..65466883,-p@chr12:65466870..65466883
-
Hg19::chr12:65466889..65466894,-p@chr12:65466889..65466894
-
Hg19::chr12:68155058..68155064,-p@chr12:68155058..68155064
-
Hg19::chr12:77730114..77730120,-p@chr12:77730114..77730120
-
Hg19::chr13:110258158..110258170,-p@chr13:110258158..110258170
-
Hg19::chr13:28541425..28541439,-p@chr13:28541425..28541439
-
Hg19::chr13:28541442..28541451,-p@chr13:28541442..28541451
-
Hg19::chr13:28541455..28541475,-p7@CDX2
Hg19::chr13:28541477..28541493,-p6@CDX2
Hg19::chr13:28542963..28542973,-p1@CU677005
Hg19::chr13:28543253..28543276,-p5@CDX2
Hg19::chr13:28543285..28543314,-p2@CDX2
Hg19::chr13:28543316..28543329,-p4@CDX2
Hg19::chr13:28543388..28543406,-p3@CDX2
Hg19::chr13:28543409..28543420,-p8@CDX2
Hg19::chr13:28543431..28543487,-p1@CDX2
Hg19::chr13:35865840..35865849,-p@chr13:35865840..35865849
-
Hg19::chr13:48703799..48703838,-p@chr13:48703799..48703838
-
Hg19::chr13:54830821..54830841,+p@chr13:54830821..54830841
+
Hg19::chr13:99661014..99661016,-p@chr13:99661014..99661016
-
Hg19::chr13:99661025..99661033,-p@chr13:99661025..99661033
-
Hg19::chr14:26793376..26793387,-p@chr14:26793376..26793387
-
Hg19::chr14:26793415..26793426,-p@chr14:26793415..26793426
-
Hg19::chr14:76289395..76289406,+p@chr14:76289395..76289406
+
Hg19::chr15:45950466..45950474,+p@chr15:45950466..45950474
+
Hg19::chr15:45950495..45950505,+p@chr15:45950495..45950505
+
Hg19::chr15:45950558..45950561,+p@chr15:45950558..45950561
+
Hg19::chr15:71524066..71524082,-p@chr15:71524066..71524082
-
Hg19::chr15:89755108..89755155,-p@chr15:89755108..89755155
-
Hg19::chr16:50278603..50278615,+p@chr16:50278603..50278615
+
Hg19::chr16:50278618..50278635,+p@chr16:50278618..50278635
+
Hg19::chr16:50278652..50278662,+p@chr16:50278652..50278662
+
Hg19::chr16:53671764..53671771,-p@chr16:53671764..53671771
-
Hg19::chr16:55344418..55344442,+p@chr16:55344418..55344442
+
Hg19::chr17:39123197..39123201,-p2@KRT39
Hg19::chr17:39556122..39556149,+p@chr17:39556122..39556149
+
Hg19::chr17:50822847..50822851,-p@chr17:50822847..50822851
-
Hg19::chr17:50906109..50906121,-p@chr17:50906109..50906121
-
Hg19::chr17:50906130..50906141,-p@chr17:50906130..50906141
-
Hg19::chr17:63557759..63557774,-p4@AXIN2
Hg19::chr17:63771073..63771114,-p@chr17:63771073..63771114
-
Hg19::chr18:13542298..13542308,+p@chr18:13542298..13542308
+
Hg19::chr18:28720966..28720970,+p@chr18:28720966..28720970
+
Hg19::chr18:28860939..28860953,-p@chr18:28860939..28860953
-
Hg19::chr18:30792468..30792481,-p@chr18:30792468..30792481
-
Hg19::chr18:39550015..39550034,+p@chr18:39550015..39550034
+
Hg19::chr18:52421471..52421476,+p@chr18:52421471..52421476
+
Hg19::chr18:53252911..53252918,-p106@TCF4
Hg19::chr1:118656031..118656034,-p@chr1:118656031..118656034
-
Hg19::chr1:118656052..118656062,-p@chr1:118656052..118656062
-
Hg19::chr1:118658073..118658082,-p@chr1:118658073..118658082
-
Hg19::chr1:119837610..119837621,+p@chr1:119837610..119837621
+
Hg19::chr1:119837632..119837659,+p@chr1:119837632..119837659
+
Hg19::chr1:119837700..119837705,+p@chr1:119837700..119837705
+
Hg19::chr1:119869755..119869768,-p2@ENST00000457719
Hg19::chr1:119869778..119869800,-p3@ENST00000457719
Hg19::chr1:119869827..119869830,-p7@ENST00000457719
Hg19::chr1:119869834..119869845,-p4@ENST00000457719
Hg19::chr1:119869846..119869867,-p1@ENST00000457719
Hg19::chr1:163338283..163338286,+p@chr1:163338283..163338286
+
Hg19::chr1:198324710..198324721,+p@chr1:198324710..198324721
+
Hg19::chr1:198324725..198324738,+p@chr1:198324725..198324738
+
Hg19::chr1:198324742..198324745,+p@chr1:198324742..198324745
+
Hg19::chr1:219739282..219739288,-p@chr1:219739282..219739288
-
Hg19::chr1:47183812..47183848,-p3@KIAA0494
Hg19::chr1:47183850..47183861,-p12@KIAA0494
Hg19::chr1:47183863..47183866,-p20@KIAA0494
Hg19::chr1:55404829..55404833,-p@chr1:55404829..55404833
-
Hg19::chr1:78621016..78621042,+p@chr1:78621016..78621042
+
Hg19::chr1:93128331..93128338,-p@chr1:93128331..93128338
-
Hg19::chr1:93128346..93128356,-p@chr1:93128346..93128356
-
Hg19::chr20:10092229..10092265,-p@chr20:10092229..10092265
-
Hg19::chr20:22034809..22034813,+p1@ENST00000449427
Hg19::chr21:37143915..37143924,-p@chr21:37143915..37143924
-
Hg19::chr2:109223595..109223610,+p19@LIMS1
Hg19::chr2:127711416..127711419,+p@chr2:127711416..127711419
+
Hg19::chr2:127711472..127711475,+p@chr2:127711472..127711475
+
Hg19::chr2:148148505..148148515,-p@chr2:148148505..148148515
-
Hg19::chr2:159306961..159306975,+p@chr2:159306961..159306975
+
Hg19::chr2:159306978..159306987,+p@chr2:159306978..159306987
+
Hg19::chr2:163302780..163302789,-p@chr2:163302780..163302789
-
Hg19::chr2:163302793..163302800,-p@chr2:163302793..163302800
-
Hg19::chr2:165424899..165424913,-p6@GRB14
Hg19::chr2:171565187..171565198,-p@chr2:171565187..171565198
-
Hg19::chr2:172822844..172822852,+p@chr2:172822844..172822852
+
Hg19::chr2:191230499..191230510,+p@chr2:191230499..191230510
+
Hg19::chr2:19707156..19707203,+p@chr2:19707156..19707203
+
Hg19::chr2:205036975..205037009,-p@chr2:205036975..205037009
-
Hg19::chr2:205099653..205099688,-p1@ENST00000419860
Hg19::chr2:205099700..205099708,-p2@ENST00000419860
Hg19::chr2:225543308..225543324,+p@chr2:225543308..225543324
+
Hg19::chr2:50452322..50452343,+p@chr2:50452322..50452343
+
Hg19::chr2:66794374..66794383,+p@chr2:66794374..66794383
+
Hg19::chr2:66794389..66794398,+p@chr2:66794389..66794398
+
Hg19::chr2:740879..740895,+p@chr2:740879..740895
+
Hg19::chr2:740910..740923,+p@chr2:740910..740923
+
Hg19::chr2:747715..747728,+p@chr2:747715..747728
+
Hg19::chr3:140054665..140054678,-p@chr3:140054665..140054678
-
Hg19::chr3:140054724..140054735,-p@chr3:140054724..140054735
-
Hg19::chr3:148164659..148164667,-p@chr3:148164659..148164667
-
Hg19::chr3:148164872..148164919,-p@chr3:148164872..148164919
-
Hg19::chr3:148165064..148165071,-p@chr3:148165064..148165071
-
Hg19::chr3:156822661..156822696,-p@chr3:156822661..156822696
-
Hg19::chr3:171088092..171088113,-p@chr3:171088092..171088113
-
Hg19::chr3:185772095..185772119,-p@chr3:185772095..185772119
-
Hg19::chr3:185823495..185823511,-p12@ETV5
Hg19::chr3:185823573..185823578,-p26@ETV5
Hg19::chr3:191000073..191000089,-p5@UTS2D
Hg19::chr3:191000091..191000117,-p1@UTS2D
Hg19::chr3:193356854..193356864,+p@chr3:193356854..193356864
+
Hg19::chr3:24797750..24797759,-p@chr3:24797750..24797759
-
Hg19::chr3:24797832..24797838,-p@chr3:24797832..24797838
-
Hg19::chr3:66354424..66354472,+p@chr3:66354424..66354472
+
Hg19::chr4:138999555..138999575,-p@chr4:138999555..138999575
-
Hg19::chr4:157174023..157174034,+p@chr4:157174023..157174034
+
Hg19::chr4:157174062..157174071,+p@chr4:157174062..157174071
+
Hg19::chr4:157174075..157174084,+p@chr4:157174075..157174084
+
Hg19::chr4:157174108..157174136,+p@chr4:157174108..157174136
+
Hg19::chr4:157174324..157174332,+p@chr4:157174324..157174332
+
Hg19::chr4:169552329..169552340,+p34@PALLD
Hg19::chr4:169559850..169559856,-p@chr4:169559850..169559856
-
Hg19::chr4:71222797..71222807,+p@chr4:71222797..71222807
+
Hg19::chr5:121814761..121814765,-p4@ENST00000503529
Hg19::chr5:121814774..121814793,-p1@ENST00000503529
p1@ENST00000510972
p1@uc003ktb.1
Hg19::chr5:57619538..57619575,-p@chr5:57619538..57619575
-
Hg19::chr5:71987749..71987774,-p@chr5:71987749..71987774
-
Hg19::chr5:97747048..97747059,+p@chr5:97747048..97747059
+
Hg19::chr6:104674708..104674749,-p@chr6:104674708..104674749
-
Hg19::chr6:372660..372670,-p@chr6:372660..372670
-
Hg19::chr6:5491056..5491061,+p@chr6:5491056..5491061
+
Hg19::chr6:5491081..5491106,+p@chr6:5491081..5491106
+
Hg19::chr6:8389087..8389116,-p@chr6:8389087..8389116
-
Hg19::chr6:8389389..8389429,-p@chr6:8389389..8389429
-
Hg19::chr6:91774965..91774974,+p@chr6:91774965..91774974
+
Hg19::chr7:110230449..110230452,-p@chr7:110230449..110230452
-
Hg19::chr7:110230549..110230565,-p@chr7:110230549..110230565
-
Hg19::chr7:138064518..138064531,-p@chr7:138064518..138064531
-
Hg19::chr7:141499716..141499722,+p@chr7:141499716..141499722
+
Hg19::chr7:30499737..30499761,+p@chr7:30499737..30499761
+
Hg19::chr7:80253387..80253419,+p4@CD36
Hg19::chr7:87049573..87049608,-p@chr7:87049573..87049608
-
Hg19::chr7:87232406..87232409,-p@chr7:87232406..87232409
-
Hg19::chr7:87232419..87232430,-p@chr7:87232419..87232430
-
Hg19::chr7:87232440..87232448,-p@chr7:87232440..87232448
-
Hg19::chr7:89797154..89797172,+p9@STEAP2
Hg19::chr8:107630340..107630359,+p12@OXR1
Hg19::chr8:107667666..107667673,+p@chr8:107667666..107667673
+
Hg19::chr8:127438794..127438800,+p@chr8:127438794..127438800
+
Hg19::chr8:127440115..127440120,+p@chr8:127440115..127440120
+
Hg19::chr8:127445866..127445873,+p@chr8:127445866..127445873
+
Hg19::chr8:127449395..127449424,+p@chr8:127449395..127449424
+
Hg19::chr8:127450087..127450092,+p@chr8:127450087..127450092
+
Hg19::chr8:127472815..127472822,+p@chr8:127472815..127472822
+
Hg19::chr8:127508635..127508640,+p@chr8:127508635..127508640
+
Hg19::chr8:127566297..127566307,-p@chr8:127566297..127566307
-
Hg19::chr8:127567083..127567087,-p6@FAM84B
Hg19::chr8:127568784..127568794,+p6@ENST00000524320
Hg19::chr8:127568810..127568821,+p2@ENST00000524320
Hg19::chr8:127569936..127570038,-p3@FAM84B
Hg19::chr8:127570603..127570648,-p1@FAM84B
Hg19::chr8:127570656..127570667,-p5@FAM84B
Hg19::chr8:127570676..127570690,-p4@FAM84B
Hg19::chr8:127570706..127570729,-p2@FAM84B
Hg19::chr8:127681013..127681042,-p@chr8:127681013..127681042
-
Hg19::chr8:127817393..127817400,+p@chr8:127817393..127817400
+
Hg19::chr8:127836882..127836885,+p@chr8:127836882..127836885
+
Hg19::chr8:127881773..127881775,+p@chr8:127881773..127881775
+
Hg19::chr8:128118744..128118753,-p@chr8:128118744..128118753
-
Hg19::chr8:128259602..128259609,-p@chr8:128259602..128259609
-
Hg19::chr8:128260156..128260173,+p@chr8:128260156..128260173
+
Hg19::chr8:128269499..128269507,-p@chr8:128269499..128269507
-
Hg19::chr8:128415915..128415922,+p@chr8:128415915..128415922
+
Hg19::chr8:128415944..128415958,+p@chr8:128415944..128415958
+
Hg19::chr8:128418204..128418209,-p@chr8:128418204..128418209
-
Hg19::chr8:128418747..128418756,-p@chr8:128418747..128418756
-
Hg19::chr8:128418776..128418790,-p@chr8:128418776..128418790
-
Hg19::chr8:128418828..128418839,-p@chr8:128418828..128418839
-
Hg19::chr8:128419359..128419367,-p@chr8:128419359..128419367
-
Hg19::chr8:128691603..128691614,-p@chr8:128691603..128691614
-
Hg19::chr8:128747729..128747748,+p14@MYC
Hg19::chr8:128747757..128747800,+p7@MYC
Hg19::chr8:128806214..128806243,+p@chr8:128806214..128806243
+
Hg19::chr8:128806244..128806266,+p@chr8:128806244..128806266
+
Hg19::chr8:128806307..128806348,+p9@PVT1
Hg19::chr8:128806753..128806815,+p1@PVT1
Hg19::chr8:128807259..128807281,+p@chr8:128807259..128807281
+
Hg19::chr8:128807937..128807941,+p20@PVT1
Hg19::chr8:128900203..128900207,+p@chr8:128900203..128900207
+
Hg19::chr8:128908624..128908634,+p@chr8:128908624..128908634
+
Hg19::chr8:128908649..128908661,+p@chr8:128908649..128908661
+
Hg19::chr8:128908678..128908696,+p@chr8:128908678..128908696
+
Hg19::chr8:128909509..128909531,+p@chr8:128909509..128909531
+
Hg19::chr8:128909572..128909583,+p@chr8:128909572..128909583
+
Hg19::chr8:128909594..128909613,+p@chr8:128909594..128909613
+
Hg19::chr8:128909653..128909681,+p@chr8:128909653..128909681
+
Hg19::chr8:128910010..128910030,+p@chr8:128910010..128910030
+
Hg19::chr8:130284717..130284721,-p@chr8:130284717..130284721
-
Hg19::chr8:39792165..39792176,+p1@IDO2
Hg19::chr8:39792182..39792188,+p14@IDO2
Hg19::chr9:104610923..104610939,-p@chr9:104610923..104610939
-
Hg19::chr9:120162674..120162685,-p@chr9:120162674..120162685
-
Hg19::chr9:125898916..125898941,-p14@STRBP
Hg19::chr9:95166976..95166979,-p8@OGN
Hg19::chr9:97766409..97766428,+p20@C9orf3
Hg19::chr9:98505341..98505348,+p@chr9:98505341..98505348
+
Hg19::chrX:138909080..138909093,-p@chrX:138909080..138909093
-
Hg19::chrX:138914394..138914405,-p10@ATP11C
Hg19::chrX:42162203..42162241,+p@chrX:42162203..42162241
+


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

p.valueFDRnGenesnPathwayName
2.05892215321743e-050.006516488614933166740TGF beta receptor down reg. targets (Netpath):NetPath_7
1.47712332636225e-060.000935019065587306328Wnt down reg. targets (Netpath):NetPath_8



Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

No GOStat results

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br>disease_data<br>

Uber Anatomy
Ontology termp-valuen
rectum3.10e-504
intestinal mucosa3.10e-504
wall of intestine3.10e-504
gastrointestinal system mucosa3.10e-504
gastrointestinal system epithelium3.10e-504
intestinal epithelium3.10e-504
lower digestive tract1.48e-405
epithelium of mucosa5.22e-268
colon2.62e-239
simple columnar epithelium2.62e-239
large intestine2.25e-1911
anatomical wall6.76e-1812
intestine1.85e-1217
hindgut6.95e-1219
mucosa2.29e-1120
gastrointestinal system4.34e-0925
Disease
Ontology termp-valuen
gastrointestinal system cancer1.43e-1514
adenocarcinoma2.15e-0925


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

Novel motifs



JASPAR motifs

Motifs-log10(p-value)
MA0003.15.78596e-16
MA0004.10.139922
MA0006.17.93973e-05
MA0007.10.596186
MA0009.10.171693
MA0014.16.74065e-14
MA0017.10.306656
MA0019.10.289807
MA0024.10.00483522
MA0025.11.84438
MA0027.11.11723
MA0028.11.46221e-07
MA0029.10.84446
MA0030.10.800621
MA0031.11.40273
MA0038.11.46595
MA0040.10.86722
MA0041.10.0161634
MA0042.10.260657
MA0043.10.172019
MA0046.10.0601223
MA0048.11.50689e-06
MA0050.10.980546
MA0051.11.71097
MA0052.10.611192
MA0055.10.000188286
MA0056.10
MA0057.10.00120573
MA0058.10.327561
MA0059.10.538972
MA0060.10.00239364
MA0061.10.0064054
MA0063.10
MA0066.10.760897
MA0067.10.0967598
MA0068.10.284478
MA0069.10.807939
MA0070.10.770065
MA0071.10.415598
MA0072.10.493968
MA0073.10
MA0074.10.0571203
MA0076.11.86545e-07
MA0077.10.276404
MA0078.10.0421982
MA0081.10.42306
MA0083.10.590267
MA0084.11.67382
MA0087.11.41702
MA0088.16.61526e-05
MA0089.10
MA0090.10.605497
MA0091.10.0510851
MA0092.10.281781
MA0093.10.17062
MA0095.10
MA0098.10
MA0100.10.0348732
MA0101.10.0879631
MA0103.10.328287
MA0105.19.39918e-07
MA0106.10.0209825
MA0107.10.0194124
MA0108.22.11273
MA0109.10
MA0111.10.424225
MA0113.10.205732
MA0114.10.0162898
MA0115.10.0678939
MA0116.10.00177228
MA0117.10.0187725
MA0119.11.38334
MA0122.10.244329
MA0124.11.65852
MA0125.12.8105
MA0130.10
MA0131.10.000660987
MA0132.10
MA0133.10
MA0135.10.395957
MA0136.10.79722
MA0139.19.69363e-05
MA0140.10.0668659
MA0141.10.659806
MA0142.14.58617
MA0143.11.36894
MA0144.10.0265573
MA0145.11.11166e-05
MA0146.19.25754e-15
MA0147.10.0594181
MA0148.10.688342
MA0149.126.025
MA0062.22.67232e-07
MA0035.20.188815
MA0039.22.84964e-12
MA0138.20.000492873
MA0002.20.267564
MA0137.20.0813758
MA0104.20.00767207
MA0047.20.711917
MA0112.20.0119828
MA0065.20.012648
MA0150.10.174113
MA0151.10
MA0152.10.430512
MA0153.11.2311
MA0154.10.000516721
MA0155.10.000103244
MA0156.10.00188964
MA0157.10.580394
MA0158.10
MA0159.10.0604569
MA0160.11.19401
MA0161.10
MA0162.11.00926e-11
MA0163.14.00196e-15
MA0164.10.705146
MA0080.20.170889
MA0018.20.0510534
MA0099.20.306163
MA0079.20
MA0102.20.212863
MA0258.10.43627
MA0259.10.00587348
MA0442.10



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

No analysis results for this cluster

Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

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